bims-camemi 2022-09-25 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2022–09–25
forty-one papers selected by
Christian Frezza, Universität zu Köln

Sensitisation of cancer cells to radiotherapy by serine and glycine starvation.
ORP5/8 and MIB/MICOS link ER-mitochondria and intra-mitochondrial contacts for non-vesicular transport of phosphatidylserine.
Evaluation of Urea Cycle Activity by Metabolic Flux Analysis Using Mass Spectrometry.
1-deoxysphingolipid synthesis compromises anchorage-independent growth and plasma membrane endocytosis in cancer cells.
Improving the reproducibility of metabolic research.
Amino acid metabolism in skeletal cells.
Novel Regulators of Macropinocytosis-Dependent Growth Revealed by Informer Set Library Screening in Pancreatic Cancer Cells.
YY1 promotes pancreatic cancer cell proliferation by enhancing mitochondrial respiration.
Metabolic collateral lethal target identification reveals MTHFD2 paralogue dependency in ovarian cancer.
Metabokines in the regulation of systemic energy metabolism.
The evolutionary dynamics of extrachromosomal DNA in human cancers.
Interplays of glucose metabolism and KRAS mutation in pancreatic ductal adenocarcinoma.
Mitochondrial Protein Cox7b Is a Metabolic Sensor Driving Brain-Specific Metastasis of Human Breast Cancer Cells.
Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function.
Flow pattern-dependent mitochondrial dynamics regulates the metabolic profile and inflammatory state of endothelial cells.
Oxygen regulation of breathing is abolished in mitochondrial complex III-deficient arterial chemoreceptors.
FAM96A is essential for maintaining organismal energy balance and adipose tissue homeostasis in mice.
The [PSI+] prion modulates cytochrome c oxidase deficiency caused by deletion of COX12.
The multiple facets of mitochondrial regulations controlling cellular thermogenesis.
NAMPT is a metabolic checkpoint of IFNγ-producing CD4+ T cells in lupus nephritis.
Mitochondrial Fission and Fusion: Molecular Mechanisms, Biological Functions, and Related Disorders.
Mitochondrial quality control mechanisms as molecular targets in diabetic heart.
The role of spatiotemporal organization and dynamics of clock complexes in circadian regulation.
CLN3 is required for the clearance of glycerophosphodiesters from lysosomes.
Pore formation-independent cell death induced by a β-barrel pore-forming toxin.
The requirement for mitochondrial respiration in cancer varies with disease stage.
The role of aging in cancer.
Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1.
Hexosamine pathway activation improves memory but does not extend lifespan in mice.
A cellular hierarchy in melanoma uncouples growth and metastasis.
A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production.
Metabolic Adaptation as Potential Target in Papillary Renal Cell Carcinomas Based on Their In Situ Metabolic Characteristics.
Oncogenic RAS commandeers amino acid sensing machinery to aberrantly activate mTORC1 in multiple myeloma.
In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer.
Renal oncometabolite L-2-hydroxyglutarate imposes a block in kidney tubulogenesis: Evidence for an epigenetic basis for the L-2HG-induced impairment of differentiation.
Lysosomal Ion Channels: What Are They Good For and Are They Druggable Targets?
The origins of medulloblastoma tumours in humans.
Revisiting life history and morphological proxies for early mammaliaform metabolic rates.
Targeting Krebs-cycle-deficient renal cell carcinoma with Poly ADP-ribose polymerase inhibitors and low-dose alkylating chemotherapy.
Thymidine rescues ATR kinase inhibitor-induced deoxyuridine contamination in genomic DNA, cell death, and interferon-α/β expression.
Sphingosine kinases regulate ER contacts with late endocytic organelles and cholesterol trafficking.

Br J Cancer. 2022 Sep 17.

Sensitisation of cancer cells to radiotherapy by serine and glycine starvation.

Mattia Falcone, Alejandro Huerta Uribe, Vasileios Papalazarou, Alice C Newman, Dimitris Athineos, Katrina Stevenson, Charles-Etienne Gabriel Sauvé, Yajing Gao, Jin K Kim, Michael Del Latto, Maria Kierstead, Chao Wu, J Joshua Smith, Paul B Romesser, Anthony J Chalmers, Karen Blyth, Oliver D K Maddocks.

BACKGROUND: Cellular metabolism is an integral component of cellular adaptation to stress, playing a pivotal role in the resistance of cancer cells to various treatment modalities, including radiotherapy. In response to radiotherapy, cancer cells engage antioxidant and DNA repair mechanisms which mitigate and remove DNA damage, facilitating cancer cell survival. Given the reliance of these resistance mechanisms on amino acid metabolism, we hypothesised that controlling the exogenous availability of the non-essential amino acids serine and glycine would radiosensitise cancer cells.
METHODS: We exposed colorectal, breast and pancreatic cancer cell lines/organoids to radiation in vitro and in vivo in the presence and absence of exogenous serine and glycine. We performed phenotypic assays for DNA damage, cell cycle, ROS levels and cell death, combined with a high-resolution untargeted LCMS metabolomics and RNA-Seq.
RESULTS: Serine and glycine restriction sensitised a range of cancer cell lines, patient-derived organoids and syngeneic mouse tumour models to radiotherapy. Comprehensive metabolomic and transcriptomic analysis of central carbon metabolism revealed that amino acid restriction impacted not only antioxidant response and nucleotide synthesis but had a marked inhibitory effect on the TCA cycle.
CONCLUSION: Dietary restriction of serine and glycine is a viable radio-sensitisation strategy in cancer.

DOI: https://doi.org/10.1038/s41416-022-01965-6
Cell Rep. 2022 Sep 20. pii: S2211-1247(22)01196-2. [Epub ahead of print]40(12): 111364

ORP5/8 and MIB/MICOS link ER-mitochondria and intra-mitochondrial contacts for non-vesicular transport of phosphatidylserine.

Vera F Monteiro-Cardoso, Leila Rochin, Amita Arora, Audrey Houcine, Eeva Jääskeläinen, Annukka M Kivelä, Cécile Sauvanet, Romain Le Bars, Eyra Marien, Jonas Dehairs, Julie Neveu, Naima El Khallouki, Elena Santonico, Johannes V Swinnen, David Tareste, Vesa M Olkkonen, Francesca Giordano.

  Mitochondria are dynamic organelles essential for cell survival whose structural and functional integrity rely on selective and regulated transport of lipids from/to the endoplasmic reticulum (ER) and across the mitochondrial intermembrane space. As they are not connected by vesicular transport, the exchange of lipids between ER and mitochondria occurs at membrane contact sites. However, the mechanisms and proteins involved in these processes are only beginning to emerge. Here, we show that the main physiological localization of the lipid transfer proteins ORP5 and ORP8 is at mitochondria-associated ER membrane (MAM) subdomains, physically linked to the mitochondrial intermembrane space bridging (MIB)/mitochondrial contact sites and cristae junction organizing system (MICOS) complexes that bridge the two mitochondrial membranes. We also show that ORP5/ORP8 mediate non-vesicular transport of phosphatidylserine (PS) lipids from the ER to mitochondria by cooperating with the MIB/MICOS complexes. Overall our study reveals a physical and functional link between ER-mitochondria contacts involved in lipid transfer and intra-mitochondrial membrane contacts maintained by the MIB/MICOS complexes.

Keywords:  CP: Cell biology; MAM; MICOS; Mic60; ORP; SAM50; cristae junctions; membrane contact sites; mitochondria; phosphatidylserine

DOI:  https://doi.org/10.1016/j.celrep.2022.111364
Methods Mol Biol. 2022 ;2544 129-144

Evaluation of Urea Cycle Activity by Metabolic Flux Analysis Using Mass Spectrometry.

Yasuharu Ueno, Takuji Maeda, Satoshi Okamoto, Hideki Taniguchi.

  Hepatocytes play an important role in maintaining homeostasis in living organisms by carrying out various metabolic functions. The urea cycle, one of the metabolic pathways taking place in hepatocytes, is an important metabolic pathway that converts toxic ammonia to nontoxic urea. Performing quantitative assessments of individual metabolite levels using a mass spectrometer is useful for assessing the metabolic state of the urea cycle in hepatocytes. In addition, metabolic flux analysis using stable isotopes and a mass spectrometer is a new technique for measuring the metabolic state. It enables conducting specific, objective, and quantitative measurement of the activated state of the target metabolic pathway regardless of external disturbing factors. This section describes the technical background and methodology of performing metabolic flux analysis of the urea cycle by mass spectrometry.

Keywords:  Hepatocytes; Metabolic flux analysis; Urea cycle

DOI:  https://doi.org/10.1007/978-1-0716-2557-6_9
J Lipid Res. 2022 Sep 14. pii: S0022-2275(22)00114-6. [Epub ahead of print] 100281

1-deoxysphingolipid synthesis compromises anchorage-independent growth and plasma membrane endocytosis in cancer cells.

Thekla Cordes, Ramya S Kuna, Grace H McGregor, Sanika V Khare, Jivani Gengatharan, Thangaselvam Muthusamy, Christian M Metallo.

  Serine palmitoyltransferase (SPT) predominantly incorporates serine and fatty acyl-CoAs into diverse sphingolipids that serve as structural components of membranes and signaling molecules within or amongst cells. However, SPT also uses alanine as a substrate in the contexts of low serine availability, alanine accumulation, or disease-causing mutations in hereditary sensory neuropathy type I (HSAN1), resulting in the synthesis and accumulation of 1-deoxysphingolipids. These species promote cytotoxicity in neurons and impact diverse cellular phenotypes, including suppression of anchorage-independent cancer cell growth. While altered serine and alanine levels can promote 1-deoxysphingolipid synthesis, they impact numerous other metabolic pathways important for cancer cells. Here we combined isotope tracing, quantitative metabolomics, and functional studies to better understand the mechanistic drivers of 1-deoxysphingolipid toxicity in cancer cells. We determined that both alanine treatment and SPTLC1C133W expression induce 1-deoxy(dihydro)ceramide synthesis and accumulation but fail to broadly impact intermediary metabolism, abundances of other lipids, or growth of adherent cells. However, we found spheroid culture and soft agar colony formation were compromised when endogenous 1-deoxysphingolipid synthesis was induced via SPTLC1C133W expression. Consistent with these impacts on anchorage-independent cell growth, we observed that 1-deoxysphingolipid synthesis reduced plasma membrane endocytosis. These results highlight a potential role for SPT promiscuity in linking altered amino acid metabolism to plasma membrane endocytosis.

Keywords:  1-deoxy(dihydro)ceramide; 1-deoxysphingolipid accumulation; Metabolism; RAB5; SPT promiscuity; alanine; mitochondrial stress; serine; serine palmitoyltransferase; soft agar

DOI:  https://doi.org/10.1016/j.jlr.2022.100281
Nat Metab. 2022 Sep;4(9): 1085

Improving the reproducibility of metabolic research.

DOI: https://doi.org/10.1038/s42255-022-00653-2
Bone Rep. 2022 Dec;17 101620

Amino acid metabolism in skeletal cells.

Claire-Sophie Devignes, Geert Carmeliet, Steve Stegen.

  Amino acid metabolism regulates essential cellular functions, not only by fueling protein synthesis, but also by supporting the biogenesis of nucleotides, redox factors and lipids. Amino acids are also involved in tricarboxylic acid cycle anaplerosis, epigenetic modifications, next to synthesis of neurotransmitters and hormones. As such, amino acids contribute to a broad range of cellular processes such as proliferation, matrix synthesis and intercellular communication, which are all critical for skeletal cell functioning. Here we summarize recent work elucidating how amino acid metabolism supports and regulates skeletal cell function during bone growth and homeostasis, as well as during skeletal disease. The most extensively studied amino acid is glutamine, and osteoblasts and chondrocytes rely heavily on this non-essential amino acid during for their functioning and differentiation. Regulated by lineage-specific transcription factors such as SOX9 and osteoanabolic agents such as parathyroid hormone or WNT, glutamine metabolism has a wide range of metabolic roles, as it fuels anabolic processes by producing nucleotides and non-essential amino acids, maintains redox balance by generating the antioxidant glutathione and regulates cell-specific gene expression via epigenetic mechanisms. We also describe how other amino acids affect skeletal cell functions, although further work is needed to fully understand their effect. The increasing number of studies using stable isotope labelling in several skeletal cell types at various stages of differentiation, together with conditional inactivation of amino acid transporters or enzymes in mouse models, will allow us to obtain a more complete picture of amino acid metabolism in skeletal cells.

Keywords:  Amino acids; Cell metabolism; Chondrocyte; Glutamine; Osteoblast; Osteoclast

DOI:  https://doi.org/10.1016/j.bonr.2022.101620
Metabolites. 2022 Sep 02. pii: 831. [Epub ahead of print]12(9):

Novel Regulators of Macropinocytosis-Dependent Growth Revealed by Informer Set Library Screening in Pancreatic Cancer Cells.

Sang Hoon Kim, Jae Ho Song, Min Ji Kim, Mun Gu Song, Angel A Ku, Sourav Bandyopadhyay, Frank McCormick, Sung Eun Kim.

  Cancer cells utilize multiple nutrient scavenging mechanisms to support growth and survival in nutrient-poor, hypoxic tumor microenvironments. Among these mechanisms, macropinocytosis has emerged as an important pathway of extracellular nutrient acquisition in cancer cells, particularly in tumors with activated RAS signaling, such as pancreatic cancer. However, the absence of a clinically available inhibitor, as well as the gap of knowledge in macropinocytosis regulation, remain a hurdle for its use for cancer therapy. Here, we use the Informer set library to identify novel regulators of macropinocytosis-dependent growth in pancreatic cancer cells. Understanding how these regulators function will allow us to provide novel opportunities for therapeutic intervention.

Keywords:  Informer set library screening; cancer metabolism; macropinocytosis; nutrient scavenging; pancreatic cancer

DOI:  https://doi.org/10.3390/metabo12090831
Cancer Cell Int. 2022 Sep 19. 22(1): 287

YY1 promotes pancreatic cancer cell proliferation by enhancing mitochondrial respiration.

Bin Li, Junyi Wang, Jing Liao, Minghui Wu, Xiangshu Yuan, Hezhi Fang, Lijun Shen, Minghua Jiang.

  KRAS-driven metabolic reprogramming is a known peculiarity features of pancreatic ductal adenocarcinoma (PDAC) cells. However, the metabolic roles of other oncogenic genes, such as YY1, in PDAC development are still unclear. In this study, we observed significantly elevated expression of YY1 in human PDAC tissues, which positively correlated with a poor disease progression. Furthermore, in vitro studies confirmed that YY1 deletion inhibited PDAC cell proliferation and tumorigenicity. Moreover, YY1 deletion led to impaired mitochondrial RNA expression, which further inhibited mitochondrial oxidative phosphorylation (OXPHOS) complex assembly and altered cellular nucleotide homeostasis. Mechanistically, the impairment of mitochondrial OXPHOS function reduced the generation of aspartate, an output of the tricarboxylic acid cycle (TCA), and resulted in the inhibition of cell proliferation owing to unavailability of aspartate-associated nucleotides. Conversely, exogenous supplementation with aspartate fully restored PDAC cell proliferation. Our findings suggest that YY1 promotes PDAC cell proliferation by enhancing mitochondrial respiration and the TCA, which favors aspartate-associated nucleotide synthesis. Thus, targeting nucleotide biosynthesis is a promising strategy for PDAC treatment.

Keywords:  Aspartate; Nucleotide metabolism; OXPHOS; PDAC; YY1

DOI:  https://doi.org/10.1186/s12935-022-02712-w
Nat Metab. 2022 Sep;4(9): 1119-1137

Metabolic collateral lethal target identification reveals MTHFD2 paralogue dependency in ovarian cancer.

Abhinav Achreja, Tao Yu, Anjali Mittal, Srinadh Choppara, Olamide Animasahun, Minal Nenwani, Fulei Wuchu, Noah Meurs, Aradhana Mohan, Jin Heon Jeon, Itisam Sarangi, Anusha Jayaraman, Sarah Owen, Reva Kulkarni, Michele Cusato, Frank Weinberg, Hye Kyong Kweon, Chitra Subramanian, Max S Wicha, Sofia D Merajver, Sunitha Nagrath, Kathleen R Cho, Analisa DiFeo, Xiongbin Lu, Deepak Nagrath.

Recurrent loss-of-function deletions cause frequent inactivation of tumour suppressor genes but often also involve the collateral deletion of essential genes in chromosomal proximity, engendering dependence on paralogues that maintain similar function. Although these paralogues are attractive anticancer targets, no methodology exists to uncover such collateral lethal genes. Here we report a framework for collateral lethal gene identification via metabolic fluxes, CLIM, and use it to reveal MTHFD2 as a collateral lethal gene in UQCR11-deleted ovarian tumours. We show that MTHFD2 has a non-canonical oxidative function to provide mitochondrial NAD+, and demonstrate the regulation of systemic metabolic activity by the paralogue metabolic pathway maintaining metabolic flux compensation. This UQCR11-MTHFD2 collateral lethality is confirmed in vivo, with MTHFD2 inhibition leading to complete remission of UQCR11-deleted ovarian tumours. Using CLIM's machine learning and genome-scale metabolic flux analysis, we elucidate the broad efficacy of targeting MTHFD2 despite distinct cancer genetic profiles co-occurring with UQCR11 deletion and irrespective of stromal compositions of tumours.

DOI: https://doi.org/10.1038/s42255-022-00636-3
Curr Opin Pharmacol. 2022 Sep 19. pii: S1471-4892(22)00113-8. [Epub ahead of print]67 102286

Metabokines in the regulation of systemic energy metabolism.

Amanda Dv MacCannell, Lee D Roberts.

Metabolism consists of life-sustaining chemical reactions involving metabolites. Historically, metabolites were defined as the intermediates or end products of metabolism and considered to be passive participants changed by metabolic processes. However, recent research has redefined how we view metabolism. There is emerging evidence of metabolites which function to mediate cellular signalling and interorgan crosstalk, regulating local metabolism and systemic physiology. These bioactive metabolite signals have been termed metabokines. Metabokines regulate diverse energy metabolism pathways across multiple tissues, including fatty acid β-oxidation, mitochondrial oxidative phosphorylation, lipolysis, glycolysis and gluconeogenesis. There is increasing impetus to uncover novel metabokine signalling axes to better understand how these may be perturbed in metabolic diseases and determine their utility as therapeutic targets.

DOI: https://doi.org/10.1016/j.coph.2022.102286
Nat Genet. 2022 Sep 19.

The evolutionary dynamics of extrachromosomal DNA in human cancers.

Joshua T Lange, John C Rose, Celine Y Chen, Yuriy Pichugin, Liangqi Xie, Jun Tang, King L Hung, Kathryn E Yost, Quanming Shi, Marcella L Erb, Utkrisht Rajkumar, Sihan Wu, Sabine Taschner-Mandl, Marie Bernkopf, Charles Swanton, Zhe Liu, Weini Huang, Howard Y Chang, Vineet Bafna, Anton G Henssen, Benjamin Werner, Paul S Mischel.

Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance-random identity by descent-is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer.

DOI: https://doi.org/10.1038/s41588-022-01177-x
Cell Death Dis. 2022 Sep 24. 13(9): 817

Interplays of glucose metabolism and KRAS mutation in pancreatic ductal adenocarcinoma.

Yu-Huei Liu, Chun-Mei Hu, Yuan-Sheng Hsu, Wen-Hwa Lee.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and deadliest cancer worldwide. The primary reasons for this are the lack of early detection methods and targeted therapy. Emerging evidence highlights the metabolic addiction of cancer cells as a potential target to combat PDAC. Oncogenic mutations of KRAS are the most common triggers that drive glucose uptake and utilization via metabolic reprogramming to support PDAC growth. Conversely, high glucose levels in the pancreatic microenvironment trigger genome instability and de novo mutations, including KRASG12D, in pancreatic cells through metabolic reprogramming. Here, we review convergent and diverse metabolic networks related to oncogenic KRAS mutations between PDAC initiation and progression, emphasizing the interplay among oncogenic mutations, glucose metabolic reprogramming, and the tumor microenvironment. Recognizing cancer-related glucose metabolism will provide a better strategy to prevent and treat the high risk PDAC population.

DOI: https://doi.org/10.1038/s41419-022-05259-w
Cancers (Basel). 2022 Sep 08. pii: 4371. [Epub ahead of print]14(18):

Mitochondrial Protein Cox7b Is a Metabolic Sensor Driving Brain-Specific Metastasis of Human Breast Cancer Cells.

Marine C N M Blackman, Tania Capeloa, Justin D Rondeau, Luca X Zampieri, Zohra Benyahia, Justine A Van de Velde, Maude Fransolet, Evangelos P Daskalopoulos, Carine Michiels, Christophe Beauloye, Pierre Sonveaux.

  Distant metastases are detrimental for cancer patients, but the increasingly early detection of tumors offers a chance for metastasis prevention. Importantly, cancers do not metastasize randomly: depending on the type of cancer, metastatic progenitor cells have a predilection for well-defined organs. This has been theorized by Stephen Paget, who proposed the "seed-and-soil hypothesis", according to which metastatic colonization occurs only when the needs of a given metastatic progenitor cell (the seed) match with the resources provided by a given organ (the soil). Here, we propose to explore the seed-and-soil hypothesis in the context of cancer metabolism, thus hypothesizing that metastatic progenitor cells must be capable of detecting the availability of metabolic resources in order to home in a secondary organ. If true, it would imply the existence of metabolic sensors. Using human triple-negative MDA-MB-231 breast cancer cells and two independent brain-seeking variants as models, we report that cyclooxygenase 7b (Cox7b), a structural component of Complex IV of the mitochondrial electron transport chain, belongs to a probably larger family of proteins responsible for breast cancer brain tropism in mice. For metastasis prevention therapy, this proof-of-principle study opens a quest for the identification of therapeutically targetable metabolic sensors that drive cancer organotropism.

Keywords:  brain metastasis; breast cancer; cancer metabolism; cyclooxygenase 7b (Cox7b); mitochondria; organotropism; oxidative phosphorylation (OXPHOS); tissue-specific metastasis

DOI:  https://doi.org/10.3390/cancers14184371
PLoS Biol. 2022 Sep;20(9): e3001753

Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function.

Neal K Bennett, Hiroki J Nakaoka, Danny Laurent, Ross A Okimoto, Yoshitaka Sei, Andrew E Horvai, Trever G Bivona, Johanna Ten Hoeve, Thomas G Graeber, Ken Nakamura, Jean L Nakamura.

The Warburg effect, aerobic glycolysis, is a hallmark feature of cancer cells grown in culture. However, the relative roles of glycolysis and respiratory metabolism in supporting in vivo tumor growth and processes such as tumor dissemination and metastatic growth remain poorly understood, particularly on a systems level. Using a CRISPRi mini-library enriched for mitochondrial ribosomal protein and respiratory chain genes in multiple human lung cancer cell lines, we analyzed in vivo metabolic requirements in xenograft tumors grown in distinct anatomic contexts. While knockdown of mitochondrial ribosomal protein and respiratory chain genes (mito-respiratory genes) has little impact on growth in vitro, tumor cells depend heavily on these genes when grown in vivo as either flank or primary orthotopic lung tumor xenografts. In contrast, respiratory function is comparatively dispensable for metastatic tumor growth. RNA-Seq and metabolomics analysis of tumor cells expressing individual sgRNAs against mito-respiratory genes indicate overexpression of glycolytic genes and increased sensitivity of glycolytic inhibition compared to control when grown in vitro, but when grown in vivo as primary tumors these cells down-regulate glycolytic mechanisms. These studies demonstrate that discrete perturbations of mitochondrial respiratory chain function impact in vivo tumor growth in a context-specific manner with differential impacts on primary and metastatic tumors.

DOI: https://doi.org/10.1371/journal.pbio.3001753
JCI Insight. 2022 Sep 22. pii: e159286. [Epub ahead of print]7(18):

Flow pattern-dependent mitochondrial dynamics regulates the metabolic profile and inflammatory state of endothelial cells.

Soon-Gook Hong, Junchul Shin, Soo Young Choi, Jeffery C Powers, Benjamin M Meister, Jacqueline Sayoc, Jun Seok Son, Ryan Tierney, Fabio A Recchia, Michael D Brown, Xiaofeng Yang, Joon-Young Park.

  Endothelial mitochondria play a pivotal role in maintaining endothelial cell (EC) homeostasis through constantly altering their size, shape, and intracellular localization. Studies show that the disruption of the basal mitochondrial network in EC, forming excess fragmented mitochondria, implicates cardiovascular disease. However, cellular consequences underlying the morphological changes in the endothelial mitochondria under distinctively different, but physiologically occurring, flow patterns (i.e., unidirectional flow [UF] versus disturbed flow [DF]) are largely unknown. The purpose of this study was to investigate the effect of different flow patterns on mitochondrial morphology and its implications in EC phenotypes. We show that mitochondrial fragmentation is increased at DF-exposed vessel regions, where elongated mitochondria are predominant in the endothelium of UF-exposed regions. DF increased dynamin-related protein 1 (Drp1), mitochondrial reactive oxygen species (mtROS), hypoxia-inducible factor 1, glycolysis, and EC activation. Inhibition of Drp1 significantly attenuated these phenotypes. Carotid artery ligation and microfluidics experiments further validate that the significant induction of mitochondrial fragmentation was associated with EC activation in a Drp1-dependent manner. Contrarily, UF in vitro or voluntary exercise in vivo significantly decreased mitochondrial fragmentation and enhanced fatty acid uptake and OXPHOS. Our data suggest that flow patterns profoundly change mitochondrial fusion/fission events, and this change contributes to the determination of proinflammatory and metabolic states of ECs.

Keywords:  Atherosclerosis; Endothelial cells; Mitochondria; Vascular Biology

DOI:  https://doi.org/10.1172/jci.insight.159286
Proc Natl Acad Sci U S A. 2022 Sep 27. 119(39): e2202178119

Oxygen regulation of breathing is abolished in mitochondrial complex III-deficient arterial chemoreceptors.

Daniel Cabello-Rivera, Patricia Ortega-Sáenz, Lin Gao, Ana M Muñoz-Cabello, Victoria Bonilla-Henao, Paul T Schumacker, José López-Barneo.

  Acute oxygen (O2) sensing is essential for adaptation of organisms to hypoxic environments or medical conditions with restricted exchange of gases in the lung. The main acute O2-sensing organ is the carotid body (CB), which contains neurosecretory chemoreceptor (glomus) cells innervated by sensory fibers whose activation by hypoxia elicits hyperventilation and increased cardiac output. Glomus cells have mitochondria with specialized metabolic and electron transport chain (ETC) properties. Reduced mitochondrial complex (MC) IV activity by hypoxia leads to production of signaling molecules (NADH and reactive O2 species) in MCI and MCIII that modulate membrane ion channel activity. We studied mice with conditional genetic ablation of MCIII that disrupts the ETC in the CB and other catecholaminergic tissues. Glomus cells survived MCIII dysfunction but showed selective abolition of responsiveness to hypoxia (increased [Ca2+] and transmitter release) with normal responses to other stimuli. Mitochondrial hypoxic NADH and reactive O2 species signals were also suppressed. MCIII-deficient mice exhibited strong inhibition of the hypoxic ventilatory response and altered acclimatization to sustained hypoxia. These data indicate that a functional ETC, with coupling between MCI and MCIV, is required for acute O2 sensing. O2 regulation of breathing results from the integrated action of mitochondrial ETC complexes in arterial chemoreceptors.

Keywords:  acute O2 sensing; carotid body glomus cell; hypoxia; mitochondrial O2 sensing and signaling; mitochondrial complex III

DOI:  https://doi.org/10.1073/pnas.2202178119
Free Radic Biol Med. 2022 Sep 20. pii: S0891-5849(22)00593-7. [Epub ahead of print]

FAM96A is essential for maintaining organismal energy balance and adipose tissue homeostasis in mice.

Zhuanzhuan Liu, Shihong Xu, Zhiwei Zhang, Hanying Wang, Qiyue Jing, Shenghan Zhang, Mengnan Liu, Jinzhi Han, Yanbo Kou, Yanxia Wei, Lu Wang, Yugang Wang.

  The iron (Fe) metabolism plays important role in regulating systemic metabolism and obesity development. The Fe inside cells can form iron-sulfur (Fe-S) clusters, which are usually assembled into target proteins with the help of a conserved cluster assembly machinery. Family with sequence similarity 96A (FAM96A; also designated CIAO2A) is a cytosolic Fe-S assembly protein involved in the regulation of cellular Fe homeostasis. However, the biological function of FAM96A in vivo is still incompletely defined. Here, we tested the role of FAM96A in regulating organismal Fe metabolism, which is relevant to obesity and adipose tissue homeostasis. We found that in mice genetically lacking FAM96A globally, intracellular Fe homeostasis was interrupted in both white and brown adipocytes, but the systemic Fe level was normal. FAM96A deficiency led to adipocyte hypertrophy and organismal energy expenditure reduction even under nonobesogenic normal chow diet-fed conditions. Mechanistically, FAM96A deficiency promoted mechanistic target of rapamycin (mTOR) signaling in adipocytes, leading to an elevation of de novo lipogenesis and, therefore, fat mass accumulation. Furthermore, it also caused mitochondrial defects, including defects in mitochondrial number, ultrastructure, redox activity, and metabolic function in brown adipocytes, which are known to be critical for the control of energy balance. Moreover, adipocyte-selective FAM96A knockout partially phenocopied global FAM96A deficiency with adipocyte hypertrophy and organismal energy expenditure defects but the mice were resistant to high-fat diet-induced weight gain. Thus, FAM96A in adipocytes may autonomously act as a critical gatekeeper of organismal energy balance by coupling Fe metabolism to adipose tissue homeostasis.

Keywords:  Adipose tissue; Energy expenditure; Iron metabolism; Iron-sulfur assembly protein; Mitochondria; brown adipocytes

DOI:  https://doi.org/10.1016/j.freeradbiomed.2022.09.011
Mol Biol Cell. 2022 Sep 21. mbcE21100499

The [PSI+] prion modulates cytochrome c oxidase deficiency caused by deletion of COX12.

Pawan Kumar Saini, Hannah Dawitz, Andreas Aufschnaiter, Stanislav Bondarev, Jinsu Thomas, Amélie Amblard, James Stewart, Nicolas Thierry-Mieg, Martin Ott, Fabien Pierrel.

Cytochrome c oxidase is a pivotal enzyme of the mitochondrial respiratory chain, which sustains bioenergetics of eukaryotic cells. Cox12, a peripheral subunit of cytochrome c oxidase, is required for full activity of the enzyme, but its exact function is unknown. Here, experimental evolution of a Saccharomyces cerevisiae Δcox12 strain for ∼300 generations allowed to restore the activity of cytochrome c oxidase. In one population, the enhanced bioenergetics was caused by a A375V mutation in the AAA+ disaggregase Hsp104. Deletion or overexpression of HSP104 also increased respiration of the Δcox12 ancestor strain. This beneficial effect of Hsp104 was related to the loss of the [PSI+] prion, which forms cytosolic amyloid aggregates of the Sup35 protein. Overall, our data demonstrate that cytosolic aggregation of a prion impairs the mitochondrial metabolism of cells defective for Cox12. These findings identify a new functional connection between cytosolic proteostasis and biogenesis of the mitochondrial respiratory chain.

DOI: https://doi.org/10.1091/mbc.E21-10-0499
Cell Mol Life Sci. 2022 Sep 20. 79(10): 525

The multiple facets of mitochondrial regulations controlling cellular thermogenesis.

Florian Beignon, Naig Gueguen, Hélène Tricoire-Leignel, César Mattei, Guy Lenaers.

  Understanding temperature production and regulation in endotherm organisms becomes a crucial challenge facing the increased frequency and intensity of heat strokes related to global warming. Mitochondria, located at the crossroad of metabolism, respiration, Ca2+ homeostasis, and apoptosis, were recently proposed to further act as cellular radiators, with an estimated inner temperature reaching 50 °C in common cell lines. This inner thermogenesis might be further exacerbated in organs devoted to produce consistent efforts as muscles, or heat as brown adipose tissue, in response to acute solicitations. Consequently, pathways promoting respiratory chain uncoupling and mitochondrial activity, such as Ca2+ fluxes, uncoupling proteins, futile cycling, and substrate supplies, provide the main processes controlling heat production and cell temperature. The mitochondrial thermogenesis might be further amplified by cytoplasmic mechanisms promoting the over-consumption of ATP pools. Considering these new thermic paradigms, we discuss here all conventional wisdoms linking mitochondrial functions to cellular thermogenesis in different physiological conditions.

Keywords:  Energy balance; Mitochondria; Temperature; Thermogenesis; Uncoupling

DOI:  https://doi.org/10.1007/s00018-022-04523-8
Mol Ther. 2022 Sep 21. pii: S1525-0016(22)00567-6. [Epub ahead of print]

NAMPT is a metabolic checkpoint of IFNγ-producing CD4+ T cells in lupus nephritis.

Mengyuan Li, Yimei Lai, Binfeng Chen, Chaohuan Guo, Mianjing Zhou, Siyuan Zhao, Shuyi Wang, Jin Li, Niansheng Yang, Hui Zhang.

  IFNγ produced by T cells represents the featured cytokine and is central to the pathogenesis of lupus nephritis (LN). Here, we identified nicotinamide phosphoribosyltransferase (NAMPT), the rate limiting enzyme in salvage NAD+ biosynthetic pathway, playing a key role in controlling IFNγ production by CD4+ T cells in LN. Our data revealed that CD4+ T cells from LN showed enhanced NAMPT-mediated NAD+ biosynthetic process, which was positively correlated with IFNγ production in CD4+ T cells. NAMPT promoted aerobic glycolysis and mitochondrial respiration in CD4+ T cells from patients with LN or MRL/lpr mice through the production of NAD+. By orchestrating metabolic fitness, NAMPT promoted translational efficiency of Ifng in CD4+ T cells. In vivo, knockdown of NAMPT by siRNA or pharmacological inhibition of NAMPT by FK866 suppressed IFNγ production in CD4+ T cells, leading to reduced inflammatory infiltrates and ameliorated kidney damage in lupus mice. Taken together, this study uncovers a metabolic checkpoint of IFNγ-producing CD4+ T cells in LN that therapeutic targeting NAMPT has the potential to normalize metabolic competence and blunt pathogenicity of CD4+ T cells in LN.

Keywords:  IFNγ expression; NAMPT; lupus nephritis; metabolic checkpoint; translation efficiency

DOI:  https://doi.org/10.1016/j.ymthe.2022.09.013
Membranes (Basel). 2022 Sep 16. pii: 893. [Epub ahead of print]12(9):

Mitochondrial Fission and Fusion: Molecular Mechanisms, Biological Functions, and Related Disorders.

Mode Al Ojaimi, Azza Salah, Ayman W El-Hattab.

  Mitochondria are dynamic organelles that undergo fusion and fission. These active processes occur continuously and simultaneously and are mediated by nuclear-DNA-encoded proteins that act on mitochondrial membranes. The balance between fusion and fission determines the mitochondrial morphology and adapts it to the metabolic needs of the cells. Therefore, these two processes are crucial to optimize mitochondrial function and its bioenergetics abilities. Defects in mitochondrial proteins involved in fission and fusion due to pathogenic variants in the genes encoding them result in disruption of the equilibrium between fission and fusion, leading to a group of mitochondrial diseases termed disorders of mitochondrial dynamics. In this review, the molecular mechanisms and biological functions of mitochondrial fusion and fission are first discussed. Then, mitochondrial disorders caused by defects in fission and fusion are summarized, including disorders related to MFN2, MSTO1, OPA1, YME1L1, FBXL4, DNM1L, and MFF genes.

Keywords:  mitochondrial diseases; mitochondrial dynamics; mitochondrial fission; mitochondrial fusion

DOI:  https://doi.org/10.3390/membranes12090893
Metabolism. 2022 Sep 17. pii: S0026-0495(22)00191-3. [Epub ahead of print] 155313

Mitochondrial quality control mechanisms as molecular targets in diabetic heart.

Xing Chang, Yukun Li, Chen Cai, Feng Wu, Jing He, Yaoyuan Zhang, Jiankai Zhong, Ying Tan, Ruxiu Liu, Hang Zhu, Hao Zhou.

  Mitochondrial dysfunction has been regarded as a hallmark of diabetic cardiomyopathy. In addition to their canonical metabolic actions, mitochondria influence various other aspects of cardiomyocyte function, including oxidative stress, iron regulation, metabolic reprogramming, intracellular signaling transduction and cell death. These effects depend on the mitochondrial quality control (MQC) system, which includes mitochondrial dynamics, mitophagy and mitochondrial biogenesis. Mitochondria are not static entities, but dynamic units that undergo fission and fusion cycles to maintain their structural integrity. Increased mitochondrial fission elevates the number of mitochondria within cardiomyocytes, a necessary step for cardiomyocyte metabolism. Enhanced mitochondrial fusion promotes communication and cooperation between pairs of mitochondria, thus facilitating mitochondrial genomic repair and maintenance. On the contrary, erroneous fission or reduced fusion promotes the formation of mitochondrial fragments that contain damaged mitochondrial DNA and exhibit impaired oxidative phosphorylation. Under normal/physiological conditions, injured mitochondria can undergo mitophagy, a degradative process that delivers poorly structured mitochondria to lysosomes. However, defective mitophagy promotes the accumulation of nonfunctional mitochondria, which may induce cardiomyocyte death. A decline in the mitochondrial population due to mitophagy can stimulate mitochondrial biogenesis), which generates new mitochondrial offspring to maintain an adequate mitochondrial number. Energy crises or ATP deficiency also increase mitochondrial biogenesis, because mitochondrial DNA encodes 13 subunits of the electron transport chain (ETC) complexes. Disrupted mitochondrial biogenesis diminishes the mitochondrial mass, accelerates mitochondrial senescence and promotes mitochondrial dysfunction. In this review, we describe the involvement of MQC in the pathogenesis of diabetic cardiomyopathy. Besides, the potential targeted therapies that could be applied to improve MQC during diabetic cardiomyopathy are also discussed and accelerate the development of cardioprotective drugs for diabetic patients.

Keywords:  Diabetic cardiomyopathy; Mitochondrial biogenesis; Mitochondrial fission; Mitochondrial fusion; Mitochondrial quality control; Mitophagy

DOI:  https://doi.org/10.1016/j.metabol.2022.155313
Curr Opin Cell Biol. 2022 Sep 17. pii: S0955-0674(22)00082-5. [Epub ahead of print]78 102129

The role of spatiotemporal organization and dynamics of clock complexes in circadian regulation.

Ye Yuan, Yangbo Xiao, Swathi Yadlapalli.

  Circadian clocks are cell autonomous timekeepers that regulate ∼24-h oscillations in the expression of many genes and control rhythms in nearly all our behavior and physiology. Almost every cell in the human body has a molecular clock and networks of cells containing clock proteins orchestrate daily rhythms in many physiological processes, from sleep-wake cycles to metabolism to immunity. All eukaryotic circadian clocks are based on transcription-translation delayed negative feedback loops in which activation of core clock genes is negatively regulated by their cognate protein products. Our current understanding of circadian clocks has been accumulated from decades of genetic and biochemical experiments, however, what remains poorly understood is how clock proteins, genes, and mRNAs are spatiotemporally organized within live clock cells and how such subcellular organization affects circadian rhythms at the single cell level. Here, we review recent progress in understanding how clock proteins and genes are spatially organized within clock cells over the circadian cycle and the role of such organization in generating circadian rhythms and highlight open questions for future studies.

Keywords:  Circadian clocks; Genome organization; Rhythmic gene transcription and repression; Subcellular location of clock proteins and genes

DOI:  https://doi.org/10.1016/j.ceb.2022.102129
Nature. 2022 Sep 21.

CLN3 is required for the clearance of glycerophosphodiesters from lysosomes.

Nouf N Laqtom, Wentao Dong, Uche N Medoh, Andrew L Cangelosi, Vimisha Dharamdasani, Sze Ham Chan, Tenzin Kunchok, Caroline A Lewis, Ivonne Heinze, Rachel Tang, Christian Grimm, An N Dang Do, Forbes D Porter, Alessandro Ori, David M Sabatini, Monther Abu-Remaileh.

Lysosomes have many roles, including degrading macromolecules and signalling to the nucleus1. Lysosomal dysfunction occurs in various human conditions, such as common neurodegenerative diseases and monogenic lysosomal storage disorders (LSDs)2-4. For most LSDs, the causal genes have been identified but, in some, the function of the implicated gene is unknown, in part because lysosomes occupy a small fraction of the cellular volume so that changes in lysosomal contents are difficult to detect. Here we develop the LysoTag mouse for the tissue-specific isolation of intact lysosomes that are compatible with the multimodal profiling of their contents. We used the LysoTag mouse to study CLN3, a lysosomal transmembrane protein with an unknown function. In children, the loss of CLN3 causes juvenile neuronal ceroid lipofuscinosis (Batten disease), a lethal neurodegenerative LSD. Untargeted metabolite profiling of lysosomes from the brains of mice lacking CLN3 revealed a massive accumulation of glycerophosphodiesters (GPDs)-the end products of glycerophospholipid catabolism. GPDs also accumulate in the lysosomes of CLN3-deficient cultured cells and we show that CLN3 is required for their lysosomal egress. Loss of CLN3 also disrupts glycerophospholipid catabolism in the lysosome. Finally, we found elevated levels of glycerophosphoinositol in the cerebrospinal fluid of patients with Batten disease, suggesting the potential use of glycerophosphoinositol as a disease biomarker. Our results show that CLN3 is required for the lysosomal clearance of GPDs and reveal Batten disease as a neurodegenerative LSD with a defect in glycerophospholipid metabolism.

DOI: https://doi.org/10.1038/s41586-022-05221-y
FASEB J. 2022 Oct;36(10): e22557

Pore formation-independent cell death induced by a β-barrel pore-forming toxin.

Deepinder Kaur, Pratima Verma, Mahendra Singh, Arpita Sharma, Kusum Lata, Arunika Mukhopadhaya, Kausik Chattopadhyay.

  Vibrio cholerae cytolysin (VCC) is a β-barrel pore-forming toxin (β-PFT). It exhibits potent hemolytic activity against erythrocytes that appears to be a direct outcome of its pore-forming functionality. However, VCC-mediated cell-killing mechanism is more complicated in the case of nucleated mammalian cells. It induces apoptosis in the target nucleated cells, mechanistic details of which are still unclear. Furthermore, it has never been explored whether the ability of VCC to trigger programmed cell death is stringently dependent on its pore-forming activity. Here, we show that VCC can evoke hallmark features of the caspase-dependent apoptotic cell death even in the absence of the pore-forming ability. Our study demonstrates that VCC mutants with abortive pore-forming hemolytic activity can trigger apoptotic cell death responses and cytotoxicity, similar to those elicited by the wild-type toxin. VCC as well as its pore formation-deficient mutants display prominent propensity to translocate to the target cell mitochondria and cause mitochondrial membrane damage. Therefore, our results for the first time reveal that VCC, despite being an archetypical β-PFT, can kill target nucleated cells independent of its pore-forming functionality. These findings are intriguing for a β-PFT, whose destination is generally expected to remain limited on the target cell membranes, and whose mode of action is commonly attributed to the membrane-damaging pore-forming ability. Taken together, our study provides critical new insights regarding distinct implications of the two important virulence functionalities of VCC for the V. cholerae pathogenesis process: hemolytic activity for iron acquisition and cytotoxicity for tissue damage by the bacteria.

Keywords:  Vibrio cholerae cytolysin; apoptosis; mitochondrial ROS; mitochondrial damage; mitochondrial membrane permeability transition; pore-forming toxin; programmed cell death

DOI:  https://doi.org/10.1096/fj.202200788R
PLoS Biol. 2022 Sep;20(9): e3001800

The requirement for mitochondrial respiration in cancer varies with disease stage.

Colin Sheehan, Alexander Muir.

The roles for glycolytic and respiratory metabolism in supporting in vivo tumor growth in different contexts are not well understood. In this issue of PLOS Biology, a new study reveals that primary and metastatic tumors demonstrate divergent metabolic requirements.

DOI: https://doi.org/10.1371/journal.pbio.3001800
Mol Oncol. 2022 Sep;16(18): 3213-3219

The role of aging in cancer.

Aaron Havas, Shanshan Yin, P D Adams.

Many cancers show an increase in incidence with age, and age is the biggest single risk factor for many cancers. However, the molecular basis of this relationship is poorly understood. Through a collection of review articles, our thematic issue discusses the link between aging and cancer in aspects including somatic mutations, proteostasis, mitochondria, metabolism, senescence, epigenetic regulation, immune regulation, DNA damage, and telomere function.

DOI: https://doi.org/10.1002/1878-0261.13302
Open Biol. 2022 Sep;12(9): 220179

Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1.

João Leandro, Susmita Khamrui, Chalada Suebsuwong, Peng-Jen Chen, Cody Secor, Tetyana Dodatko, Chunli Yu, Roberto Sanchez, Robert J DeVita, Sander M Houten, Michael B Lazarus.

  In humans, a single enzyme 2-aminoadipic semialdehyde synthase (AASS) catalyses the initial two critical reactions in the lysine degradation pathway. This enzyme evolved to be a bifunctional enzyme with both lysine-2-oxoglutarate reductase (LOR) and saccharopine dehydrogenase domains (SDH). Moreover, AASS is a unique drug target for inborn errors of metabolism such as glutaric aciduria type 1 that arise from deficiencies downstream in the lysine degradation pathway. While work has been done to elucidate the SDH domain structurally and to develop inhibitors, neither has been done for the LOR domain. Here, we purify and characterize LOR and show that it is activated by alkylation of cysteine 414 by N-ethylmaleimide. We also provide evidence that AASS is rate-limiting upon high lysine exposure of mice. Finally, we present the crystal structure of the human LOR domain. Our combined work should enable future efforts to identify inhibitors of this novel drug target.

Keywords:  assay development; crystal structure; enzymology; glutaric aciduria; inborn errors of metabolism; lysine metabolism

DOI:  https://doi.org/10.1098/rsob.220179
Aging Cell. 2022 Sep 19. e13711

Hexosamine pathway activation improves memory but does not extend lifespan in mice.

Kira Allmeroth, Matías D Hartman, Martin Purrio, Andrea Mesaros, Martin S Denzel.

  Glucosamine feeding and genetic activation of the hexosamine biosynthetic pathway (HBP) have been linked to improved protein quality control and lifespan extension. However, as an energy sensor, the HBP has been implicated in tumor progression and diabetes. Given these opposing outcomes, it is imperative to explore the long-term effects of chronic HBP activation in mammals. Thus, we asked if HBP activation affects metabolism, coordination, memory, and survival in mice. N-acetyl-D-glucosamine (GlcNAc) supplementation in the drinking water had no adverse effect on weight in males but increased weight in young females. Glucose or insulin tolerance was not affected up to 20 months of age. Of note, we observed improved memory in young male mice supplemented with GlcNAc. Survival was not changed by GlcNAc treatment. To assess the effects of genetic HBP activation, we overexpressed the pathway's key enzyme GFAT1 and a constitutively activated mutant form in all mouse tissues. We detected elevated levels of the HBP product UDP-GlcNAc in mouse brains, but did not find any effects on behavior, memory, or survival. Together, while dietary GlcNAc supplementation did not extend survival in mice, it positively affected memory and is generally well tolerated.

Keywords:  GFAT1; hexosamine biosynthetic pathway; memory; metabolism; mouse survival

DOI:  https://doi.org/10.1111/acel.13711
Nature. 2022 Sep 21.

A cellular hierarchy in melanoma uncouples growth and metastasis.

Panagiotis Karras, Ignacio Bordeu, Joanna Pozniak, Ada Nowosad, Cecilia Pazzi, Nina Van Raemdonck, Ewout Landeloos, Yannick Van Herck, Dennis Pedri, Greet Bervoets, Samira Makhzami, Jia Hui Khoo, Benjamin Pavie, Jochen Lamote, Oskar Marin-Bejar, Michael Dewaele, Han Liang, Xingju Zhang, Yichao Hua, Jasper Wouters, Robin Browaeys, Gabriele Bergers, Yvan Saeys, Francesca Bosisio, Joost van den Oord, Diether Lambrechts, Anil K Rustgi, Oliver Bechter, Cedric Blanpain, Benjamin D Simons, Florian Rambow, Jean-Christophe Marine.

Although melanoma is notorious for its high degree of heterogeneity and plasticity1,2, the origin and magnitude of cell-state diversity remains poorly understood. Equally, it is unclear whether growth and metastatic dissemination are supported by overlapping or distinct melanoma subpopulations. Here, by combining mouse genetics, single-cell and spatial transcriptomics, lineage tracing and quantitative modelling, we provide evidence of a hierarchical model of tumour growth that mirrors the cellular and molecular logic underlying the cell-fate specification and differentiation of the embryonic neural crest. We show that tumorigenic competence is associated with a spatially localized perivascular niche, a phenotype acquired through an intercellular communication pathway established by endothelial cells. Consistent with a model in which only a fraction of cells are fated to fuel growth, temporal single-cell tracing of a population of melanoma cells with a mesenchymal-like state revealed that these cells do not contribute to primary tumour growth but, instead, constitute a pool of metastatic initiating cells that switch cell identity while disseminating to secondary organs. Our data provide a spatially and temporally resolved map of the diversity and trajectories of melanoma cell states and suggest that the ability to support growth and metastasis are limited to distinct pools of cells. The observation that these phenotypic competencies can be dynamically acquired after exposure to specific niche signals warrant the development of therapeutic strategies that interfere with the cancer cell reprogramming activity of such microenvironmental cues.

DOI: https://doi.org/10.1038/s41586-022-05242-7
Nat Commun. 2022 Sep 19. 13(1): 5491

A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production.

Naomi R Genuth, Zhen Shi, Koshi Kunimoto, Victoria Hung, Adele F Xu, Craig H Kerr, Gerald C Tiu, Juan A Oses-Prieto, Rachel E A Salomon-Shulman, Jeffrey D Axelrod, Alma L Burlingame, Kyle M Loh, Maria Barna.

Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control cell fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem cell differentiation, we identify dozens of ribosome composition changes underlying cell fate specification. We observe upregulation of RPL10A/uL1-containing ribosomes in the primitive streak followed by progressive decreases during mesoderm differentiation. An Rpl10a loss-of-function allele in mice causes striking early mesodermal phenotypes, including posterior trunk truncations, and inhibits paraxial mesoderm production in culture. Ribosome profiling in Rpl10a loss-of-function mice reveals decreased translation of mesoderm regulators, including Wnt pathway mRNAs, which are also enriched on RPL10A/uL1-containing ribosomes. We further show that RPL10A/uL1 regulates canonical and non-canonical Wnt signaling during stem cell differentiation and in the developing embryo. These findings reveal unexpected ribosome composition modularity that controls differentiation and development through the specialized translation of key signaling networks.

DOI: https://doi.org/10.1038/s41467-022-33263-3
Int J Mol Sci. 2022 Sep 13. pii: 10587. [Epub ahead of print]23(18):

Metabolic Adaptation as Potential Target in Papillary Renal Cell Carcinomas Based on Their In Situ Metabolic Characteristics.

Ildikó Krencz, Enikő Vetlényi, Titanilla Dankó, Gábor Petővári, Dorottya Moldvai, Dániel Sztankovics, Regina Raffay, Katalin Mészáros, Endre Sebestyén, Gyula Végső, Judit Pápay, Anna Sebestyén.

  Metabolic characteristics of kidney cancers have mainly been obtained from the most frequent clear cell renal cell carcinoma (CCRCC) studies. Moreover, the bioenergetic perturbances that affect metabolic adaptation possibilities of papillary renal cell carcinoma (PRCC) have not yet been detailed. Therefore, our study aimed to analyze the in situ metabolic features of PRCC vs. CCRCC tissues and compared the metabolic characteristics of PRCC, CCRCC, and normal tubular epithelial cell lines. The protein and mRNA expressions of the molecular elements in mammalian target of rapamycin (mTOR) and additional metabolic pathways were analyzed in human PRCC cases compared to CCRCC. The metabolic protein expression pattern, metabolite content, mTOR, and metabolic inhibitor sensitivity of renal carcinoma cell lines were also studied and compared with tubular epithelial cells, as "normal" control. We observed higher protein expressions of the "alternative bioenergetic pathway" elements, in correlation with the possible higher glutamine and acetate consumption in PRCC cells instead of higher glycolytic and mTOR activity in CCRCCs. Increased expression of certain metabolic pathway markers correlates with the detected differences in metabolite ratios, as well. The lower lactate/pyruvate, lactate/malate, and higher pyruvate/citrate intracellular metabolite ratios in PRCC compared to CCRCC cell lines suggest that ACHN (PRCC) have lower Warburg glycolytic capacity, less pronounced pyruvate to lactate producing activity and shifted OXPHOS phenotype. However, both studied renal carcinoma cell lines showed higher mTOR activity than tubular epithelial cells cultured in vitro, the metabolite ratio, the enzyme expression profiles, and the higher mitochondrial content also suggest increased importance of mitochondrial functions, including mitochondrial OXPHOS in PRCCs. Additionally, PRCC cells showed significant mTOR inhibitor sensitivity and the used metabolic inhibitors increased the effect of rapamycin in combined treatments. Our study revealed in situ metabolic differences in mTOR and metabolic protein expression patterns of human PRCC and CCRCC tissues as well as in cell lines. These underline the importance in the development of specific new treatment strategies, new mTOR inhibitors, and other anti-metabolic drug combinations in PRCC therapy.

Keywords:  in situ expression and in vitro studies; mTOR; metabolism; papillary renal cell carcinoma

DOI:  https://doi.org/10.3390/ijms231810587
Nat Commun. 2022 Sep 17. 13(1): 5469

Oncogenic RAS commandeers amino acid sensing machinery to aberrantly activate mTORC1 in multiple myeloma.

Yandan Yang, Arnold Bolomsky, Thomas Oellerich, Ping Chen, Michele Ceribelli, Björn Häupl, George W Wright, James D Phelan, Da Wei Huang, James W Lord, Callie K Van Winkle, Xin Yu, Jan Wisniewski, James Q Wang, Frances A Tosto, Erin Beck, Kelli Wilson, Crystal McKnight, Jameson Travers, Carleen Klumpp-Thomas, Grace A Smith, Stefania Pittaluga, Irina Maric, Dickran Kazandjian, Craig J Thomas, Ryan M Young.

Oncogenic RAS mutations are common in multiple myeloma (MM), an incurable malignancy of plasma cells. However, the mechanisms of pathogenic RAS signaling in this disease remain enigmatic and difficult to inhibit therapeutically. We employ an unbiased proteogenomic approach to dissect RAS signaling in MM. We discover that mutant isoforms of RAS organize a signaling complex with the amino acid transporter, SLC3A2, and MTOR on endolysosomes, which directly activates mTORC1 by co-opting amino acid sensing pathways. MM tumors with high expression of mTORC1-dependent genes are more aggressive and enriched in RAS mutations, and we detect interactions between RAS and MTOR in MM patient tumors harboring mutant RAS isoforms. Inhibition of RAS-dependent mTORC1 activity synergizes with MEK and ERK inhibitors to quench pathogenic RAS signaling in MM cells. This study redefines the RAS pathway in MM and provides a mechanistic and rational basis to target this mode of RAS signaling.

DOI: https://doi.org/10.1038/s41467-022-33142-x
Nat Immunol. 2022 Sep 23.

In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer.

Juan Dubrot, Peter P Du, Sarah Kate Lane-Reticker, Emily A Kessler, Audrey J Muscato, Arnav Mehta, Samuel S Freeman, Peter M Allen, Kira E Olander, Kyle M Ockerman, Clara H Wolfe, Fabius Wiesmann, Nelson H Knudsen, Hsiao-Wei Tsao, Arvin Iracheta-Vellve, Emily M Schneider, Andrea N Rivera-Rosario, Ian C Kohnle, Hans W Pope, Austin Ayer, Gargi Mishra, Margaret D Zimmer, Sarah Y Kim, Animesh Mahapatra, Hakimeh Ebrahimi-Nik, Dennie T Frederick, Genevieve M Boland, W Nicholas Haining, David E Root, John G Doench, Nir Hacohen, Kathleen B Yates, Robert T Manguso.

The immune system can eliminate tumors, but checkpoints enable immune escape. Here, we identify immune evasion mechanisms using genome-scale in vivo CRISPR screens across cancer models treated with immune checkpoint blockade (ICB). We identify immune evasion genes and important immune inhibitory checkpoints conserved across cancers, including the non-classical major histocompatibility complex class I (MHC class I) molecule Qa-1b/HLA-E. Surprisingly, loss of tumor interferon-γ (IFNγ) signaling sensitizes many models to immunity. The immune inhibitory effects of tumor IFN sensing are mediated through two mechanisms. First, tumor upregulation of classical MHC class I inhibits natural killer cells. Second, IFN-induced expression of Qa-1b inhibits CD8+ T cells via the NKG2A/CD94 receptor, which is induced by ICB. Finally, we show that strong IFN signatures are associated with poor response to ICB in individuals with renal cell carcinoma or melanoma. This study reveals that IFN-mediated upregulation of classical and non-classical MHC class I inhibitory checkpoints can facilitate immune escape.

DOI: https://doi.org/10.1038/s41590-022-01315-x
Front Endocrinol (Lausanne). 2022 ;13 932286

Renal oncometabolite L-2-hydroxyglutarate imposes a block in kidney tubulogenesis: Evidence for an epigenetic basis for the L-2HG-induced impairment of differentiation.

Mary Taub, Nader H Mahmoudzadeh, Jason M Tennessen, Sunil Sudarshan.

  2-Hydroxyglutarate (2HG) overproducing tumors arise in a number of tissues, including the kidney. The tumorigenesis resulting from overproduced 2HG has been attributed to the ability of 2HG alter gene expression by inhibiting α-ketoglutarate (αKG)-dependent dioxygenases, including Ten-eleven-Translocation (TET) enzymes. Genes that regulate cellular differentiation are reportedly repressed, blocking differentiation of mesenchymal cells into myocytes, and adipocytes. In this report, the expression of the enzyme responsible for L2HG degradation, L-2HG dehydrogenase (L2HGDH), is knocked down, using lentiviral shRNA, as well as siRNA, in primary cultures of normal Renal Proximal Tubule (RPT) cells. The knockdown (KD) results in increased L-2HG levels, decreased demethylation of 5mC in genomic DNA, and increased methylation of H3 Histones. Consequences include reduced tubulogenesis by RPT cells in matrigel, and reduced expression of molecular markers of differentiation, including membrane transporters as well as HNF1α and HNF1β, which regulate their transcription. These results are consistent with the hypothesis that oncometabolite 2HG blocks RPT differentiation by altering the methylation status of chromatin in a manner that impedes the transcriptional events required for normal differentiation. Presumably, similar alterations are responsible for promoting the expansion of renal cancer stem-cells, increasing their propensity for malignant transformation.

Keywords:  L-2-Hydroxyglutarate; differentiation; matrigel (MA); proximal tubule; renal cell carcinoma

DOI:  https://doi.org/10.3389/fendo.2022.932286
Annu Rev Pharmacol Toxicol. 2022 Sep 23.

Lysosomal Ion Channels: What Are They Good For and Are They Druggable Targets?

Erika Riederer, Chunlei Cang, Dejian Ren.

Lysosomes play fundamental roles in material digestion, cellular clearance, recycling, exocytosis, wound repair, Ca2+ signaling, nutrient signaling, and gene expression regulation. The organelle also serves as a hub for important signaling networks involving the mTOR and AKT kinases. Electrophysiological recording and molecular and structural studies in the past decade have uncovered several unique lysosomal ion channels and transporters, including TPCs, TMEM175, TRPMLs, CLN7, and CLC-7. They underlie the organelle's permeability to major ions, including K+, Na+, H+, Ca2+, and Cl-. The channels are regulated by numerous cellular factors, ranging from H+ in the lumen and voltage across the lysosomal membrane to ATP in the cytosol to growth factors outside the cell. Genetic variations in the channel/transporter genes are associated with diseases that include lysosomal storage diseases and neurodegenerative diseases. Recent studies with human genetics and channel activators suggest that lysosomal channels may be attractive targets for the development of therapeutics for the prevention of and intervention in human diseases. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 63 is January 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-pharmtox-051921-013755
Nature. 2022 Sep 21.

The origins of medulloblastoma tumours in humans.

Timothy N Phoenix.



Keywords:  Cancer; Medical research

DOI:  https://doi.org/10.1038/d41586-022-02951-x
Nat Commun. 2022 Sep 23. 13(1): 5562

Revisiting life history and morphological proxies for early mammaliaform metabolic rates.

Shai Meiri, Eran Levin.

DOI: https://doi.org/10.1038/s41467-022-32715-0
Oncotarget. 2022 ;13 1054-1067

Targeting Krebs-cycle-deficient renal cell carcinoma with Poly ADP-ribose polymerase inhibitors and low-dose alkylating chemotherapy.

Daiki Ueno, Juan C Vasquez, Amrita Sule, Jiayu Liang, Jinny van Doorn, Ranjini Sundaram, Sam Friedman, Randy Caliliw, Shinji Ohtake, Xun Bao, Jing Li, Huihui Ye, Karla Boyd, Rong Rong Huang, Jack Dodson, Paul Boutros, Ranjit S Bindra, Brian Shuch.

  Loss-of-function mutations in genes encoding the Krebs cycle enzymes Fumarate Hydratase (FH) and Succinate Dehydrogenase (SDH) induce accumulation of fumarate and succinate, respectively and predispose patients to hereditary cancer syndromes including the development of aggressive renal cell carcinoma (RCC). Fumarate and succinate competitively inhibit αKG-dependent dioxygenases, including Lysine-specific demethylase 4A/B (KDM4A/B), leading to suppression of the homologous recombination (HR) DNA repair pathway. In this study, we have developed new syngeneic Fh1- and Sdhb-deficient murine models of RCC, which demonstrate the expected accumulation of fumarate and succinate, alterations in the transcriptomic and methylation profile, and an increase in unresolved DNA double-strand breaks (DSBs). The efficacy of poly ADP-ribose polymerase inhibitors (PARPis) and temozolomide (TMZ), alone and in combination, was evaluated both in vitro and in vivo. Combination treatment with PARPi and TMZ results in marked in vitro cytotoxicity in Fh1- and Sdhb-deficient cells. In vivo, treatment with standard dosing of the PARP inhibitor BGB-290 and low-dose TMZ significantly inhibits tumor growth without a significant increase in toxicity. These findings provide the basis for a novel therapeutic strategy exploiting HR deficiency in FH and SDH-deficient RCC with combined PARP inhibition and low-dose alkylating chemotherapy.

Keywords:  FH; PARP inhibitor; SDHB; renal cell carcinoma; temozolomide

DOI:  https://doi.org/10.18632/oncotarget.28273
Cell Rep. 2022 Sep 20. pii: S2211-1247(22)01203-7. [Epub ahead of print]40(12): 111371

Thymidine rescues ATR kinase inhibitor-induced deoxyuridine contamination in genomic DNA, cell death, and interferon-α/β expression.

Norie Sugitani, Frank P Vendetti, Andrew J Cipriano, Pinakin Pandya, Joshua J Deppas, Tatiana N Moiseeva, Sandra Schamus-Haynes, Yiyang Wang, Drake Palmer, Hatice U Osmanbeyoglu, Anna Bostwick, Nathaniel W Snyder, Yi-Nan Gong, Katherine M Aird, Greg M Delgoffe, Jan H Beumer, Christopher J Bakkenist.

  ATR kinase is a central regulator of the DNA damage response (DDR) and cell cycle checkpoints. ATR kinase inhibitors (ATRi's) combine with radiation to generate CD8+ T cell-dependent responses in mouse models of cancer. We show that ATRi's induce cyclin-dependent kinase 1 (CDK1)-dependent origin firing across active replicons in CD8+ T cells activated ex vivo while simultaneously decreasing the activity of rate-limiting enzymes for nucleotide biosynthesis. These pleiotropic effects of ATRi induce deoxyuridine (dU) contamination in genomic DNA, R loops, RNA-DNA polymerase collisions, and interferon-α/β (IFN-α/β). Remarkably, thymidine rescues ATRi-induced dU contamination and partially rescues death and IFN-α/β expression in proliferating CD8+ T cells. Thymidine also partially rescues ATRi-induced cancer cell death. We propose that ATRi-induced dU contamination contributes to dose-limiting leukocytopenia and inflammation in the clinic and CD8+ T cell-dependent anti-tumor responses in mouse models. We conclude that ATR is essential to limit dU contamination in genomic DNA and IFN-α/β expression.

Keywords:  ATR/origin firing/deoxyuridine contamination/IFN-α/β; CP: Cancer; CP: Immunology

DOI:  https://doi.org/10.1016/j.celrep.2022.111371
Proc Natl Acad Sci U S A. 2022 Sep 27. 119(39): e2204396119

Sphingosine kinases regulate ER contacts with late endocytic organelles and cholesterol trafficking.

Elisa N D Palladino, Tytus Bernas, Christopher D Green, Cynthia Weigel, Sandeep K Singh, Can E Senkal, Andrea Martello, John P Kennelly, Erhard Bieberich, Peter Tontonoz, David A Ford, Sheldon Milstien, Emily R Eden, Sarah Spiegel.

  Membrane contact sites (MCS), close membrane apposition between organelles, are platforms for interorganellar transfer of lipids including cholesterol, regulation of lipid homeostasis, and co-ordination of endocytic trafficking. Sphingosine kinases (SphKs), two isoenzymes that phosphorylate sphingosine to the bioactive sphingosine-1-phosphate (S1P), have been implicated in endocytic trafficking. However, the physiological functions of SphKs in regulation of membrane dynamics, lipid trafficking and MCS are not known. Here, we report that deletion of SphKs decreased S1P with concomitant increases in its precursors sphingosine and ceramide, and markedly reduced endoplasmic reticulum (ER) contacts with late endocytic organelles. Expression of enzymatically active SphK1, but not catalytically inactive, rescued the deficit of these MCS. Although free cholesterol accumulated in late endocytic organelles in SphK null cells, surprisingly however, cholesterol transport to the ER was not reduced. Importantly, deletion of SphKs promoted recruitment of the ER-resident cholesterol transfer protein Aster-B (also called GRAMD1B) to the plasma membrane (PM), consistent with higher accessible cholesterol and ceramide at the PM, to facilitate cholesterol transfer from the PM to the ER. In addition, ceramide enhanced in vitro binding of the Aster-B GRAM domain to phosphatidylserine and cholesterol liposomes. Our study revealed a previously unknown role for SphKs and sphingolipid metabolites in governing diverse MCS between the ER network and late endocytic organelles versus the PM to control the movement of cholesterol between distinct cell membranes.

Keywords:  Aster-B/GRAMD1b; cholesterol; membrane contact sites; sphingolipids; sphingosine kinase

DOI:  https://doi.org/10.1073/pnas.2204396119